Variant report

Variant	rs12654798
Chromosome Location	chr5:43109783-43109784
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43091526..43093494-chr5:43109085..43110636,2	K562	blood:
2	chr5:43109727..43112275-chr5:43377801..43380719,2	K562	blood:
3	chr5:43108517..43110178-chr5:43120166..43121777,2	K562	blood:
4	chr5:43041769..43043458-chr5:43108775..43111084,2	MCF-7	breast:
5	chr5:43091526..43093622-chr5:43109085..43111256,2	K562	blood:
6	chr5:43105728..43107358-chr5:43108902..43110996,2	MCF-7	breast:
7	chr5:43105944..43108297-chr5:43109238..43111708,2	K562	blood:
8	chr5:43103618..43114075-chr5:43115760..43123048,23	MCF-7	breast:
9	chr5:43105107..43107712-chr5:43109708..43111277,2	K562	blood:
10	chr5:43065870..43068626-chr5:43108656..43111085,2	MCF-7	breast:
11	chr5:43103922..43107081-chr5:43109659..43112265,3	MCF-7	breast:
12	chr5:43065957..43068100-chr5:43108187..43111069,2	K562	blood:
13	chr5:43107258..43109995-chr5:43119020..43121426,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000172262	Chromatin interaction
ENSG00000177721	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000215068	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1001717	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs10064089	0.83[JPT][hapmap]
rs12652363	0.89[ASN][1000 genomes]
rs12653864	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12659721	0.92[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13153077	0.85[ASN][1000 genomes]
rs13153860	0.85[ASN][1000 genomes]
rs13154654	0.88[ASN][1000 genomes]
rs13159390	0.87[ASN][1000 genomes]
rs13161127	0.87[ASN][1000 genomes]
rs13163892	0.85[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs13164183	0.84[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs13164889	0.84[CHB][hapmap]
rs13166780	0.87[ASN][1000 genomes]
rs13171253	0.84[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs13172378	0.87[ASN][1000 genomes]
rs13174772	0.88[ASN][1000 genomes]
rs13178478	0.85[ASN][1000 genomes]
rs13181290	0.87[ASN][1000 genomes]
rs13182652	0.87[ASN][1000 genomes]
rs13186549	0.83[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs13189565	0.85[ASN][1000 genomes]
rs13189574	0.87[ASN][1000 genomes]
rs13190109	0.85[ASN][1000 genomes]
rs16873177	0.85[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs17242731	0.85[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs17242995	0.84[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs17243023	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs17243086	0.84[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs17243165	0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs17243515	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs17302596	0.85[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs17302931	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs186322	0.91[JPT][hapmap]
rs2291632	0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28548198	0.87[ASN][1000 genomes]
rs34071473	0.87[ASN][1000 genomes]
rs34205479	0.87[ASN][1000 genomes]
rs34242142	0.85[ASN][1000 genomes]
rs34258100	0.85[ASN][1000 genomes]
rs34302880	0.81[ASN][1000 genomes]
rs34333393	0.87[ASN][1000 genomes]
rs34448278	0.85[ASN][1000 genomes]
rs34552214	0.87[ASN][1000 genomes]
rs34924673	0.82[ASN][1000 genomes]
rs34973629	0.87[ASN][1000 genomes]
rs34992478	0.87[ASN][1000 genomes]
rs35018789	0.87[ASN][1000 genomes]
rs35106307	0.85[ASN][1000 genomes]
rs35199583	0.87[ASN][1000 genomes]
rs35230086	0.87[ASN][1000 genomes]
rs35285338	0.85[ASN][1000 genomes]
rs35397154	0.84[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs35645372	0.85[ASN][1000 genomes]
rs35665483	0.87[ASN][1000 genomes]
rs35673052	0.85[ASN][1000 genomes]
rs35754881	0.87[ASN][1000 genomes]
rs35839054	0.82[ASN][1000 genomes]
rs35855029	0.85[ASN][1000 genomes]
rs35859204	0.83[ASN][1000 genomes]
rs35949944	0.87[ASN][1000 genomes]
rs35998500	0.87[ASN][1000 genomes]
rs36122541	0.87[ASN][1000 genomes]
rs36125638	0.85[ASN][1000 genomes]
rs3752831	0.84[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3752832	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs3797306	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs3797307	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs3797308	0.85[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs3797309	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs56889091	0.85[ASN][1000 genomes]
rs56923657	0.87[ASN][1000 genomes]
rs58028166	0.85[ASN][1000 genomes]
rs585302	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6451670	0.89[ASN][1000 genomes]
rs67190423	0.87[ASN][1000 genomes]
rs67596313	0.87[ASN][1000 genomes]
rs71590635	0.87[ASN][1000 genomes]
rs71627578	0.89[ASN][1000 genomes]
rs71627579	0.87[ASN][1000 genomes]
rs71627580	0.87[ASN][1000 genomes]
rs71627583	0.87[ASN][1000 genomes]
rs71627584	0.87[ASN][1000 genomes]
rs71627585	0.85[ASN][1000 genomes]
rs71627586	0.85[ASN][1000 genomes]
rs71627587	0.82[ASN][1000 genomes]
rs72748883	0.89[ASN][1000 genomes]
rs72748886	0.85[ASN][1000 genomes]
rs72748897	0.87[ASN][1000 genomes]
rs72750704	0.86[ASN][1000 genomes]
rs72750764	0.87[ASN][1000 genomes]
rs72750780	0.87[ASN][1000 genomes]
rs73092493	0.89[ASN][1000 genomes]
rs782988	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv830274	chr5:43095551-43226087	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	138 gene(s)	inside rSNPs	diseases
9	nsv981009	chr5:43101558-43114874	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43106000-43110400	Weak transcription	Fetal Thymus	thymus
2	chr5:43106000-43120400	Weak transcription	Fetal Brain Female	brain
3	chr5:43106000-43120600	Weak transcription	Left Ventricle	heart
4	chr5:43106200-43120400	Weak transcription	Fetal Stomach	stomach
5	chr5:43106400-43110200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr5:43106400-43110800	Weak transcription	Thymus	Thymus
7	chr5:43106400-43116200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:43106400-43120400	Weak transcription	Fetal Intestine Small	intestine
9	chr5:43106600-43110400	Weak transcription	Fetal Intestine Large	intestine
10	chr5:43106600-43110800	Weak transcription	HepG2	liver
11	chr5:43106600-43111200	Weak transcription	K562	blood
12	chr5:43106600-43120400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:43108600-43111800	Enhancers	Primary T cells fromperipheralblood	blood
14	chr5:43108800-43110600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr5:43108800-43111200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:43108800-43111600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr5:43109000-43111400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:43109000-43111400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr5:43109200-43111600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr5:43109400-43111400	Enhancers	Primary T cells from cord blood	blood
21	chr5:43109400-43111600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr5:43109600-43109800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr5:43109600-43110200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr5:43109600-43110200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr5:43109600-43110200	Enhancers	Dnd41	blood
26	chr5:43109600-43111600	Enhancers	GM12878-XiMat	blood

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